PAX1 (paired box 1) - Rat Genome Database

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Gene: PAX1 (paired box 1) Sus scrofa
Analyze
Symbol: PAX1
Name: paired box 1
RGD ID: 14157214
Description: ENCODES a protein that exhibits sequence-specific double-stranded DNA binding (ortholog); INVOLVED IN bone morphogenesis (ortholog); CD4-positive, alpha-beta T cell differentiation (ortholog); CD8-positive, alpha-beta T cell differentiation (ortholog); ASSOCIATED WITH genetic disease (ortholog); Goldenhar syndrome (ortholog); Otofaciocervical Syndrome 1 (ortholog); FOUND IN nucleus (inferred)
Type: protein-coding
RefSeq Status: MODEL
Previously known as: paired box protein Pax-1
RGD Orthologs
Human
Mouse
Rat
Chinchilla
Bonobo
Dog
Squirrel
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: Sscrofa11.1 - Pig Sscrofa11.1 Assembly
Position:
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1729,422,129 - 29,431,990 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11729,421,117 - 29,436,481 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21733,372,514 - 33,386,866 (+)NCBISscrofa10.2Sscrofa10.2susScr3
JBrowse: View Region in Genome Browser (JBrowse)
Model


References
Additional References at PubMed
PMID:30032202  


Genomics

Comparative Map Data
PAX1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1729,422,129 - 29,431,990 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11729,421,117 - 29,436,481 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21733,372,514 - 33,386,866 (+)NCBISscrofa10.2Sscrofa10.2susScr3
PAX1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh382021,705,664 - 21,718,481 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl2021,705,659 - 21,718,481 (+)EnsemblGRCh38hg38GRCh38
GRCh372021,686,302 - 21,699,119 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 362021,634,297 - 21,644,620 (+)NCBINCBI36Build 36hg18NCBI36
Build 342021,635,074 - 21,643,441NCBI
Celera2021,760,205 - 21,770,528 (+)NCBICelera
Cytogenetic Map20p11.22NCBI
HuRef2021,649,121 - 21,661,830 (+)NCBIHuRef
CHM1_12021,686,612 - 21,699,440 (+)NCBICHM1_1
T2T-CHM13v2.02021,762,357 - 21,775,174 (+)NCBIT2T-CHM13v2.0
Pax1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm392147,203,850 - 147,216,972 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl2147,203,845 - 147,235,215 (+)EnsemblGRCm39 Ensembl
GRCm382147,361,930 - 147,375,049 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl2147,361,925 - 147,393,295 (+)EnsemblGRCm38mm10GRCm38
MGSCv372147,190,730 - 147,200,785 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv362147,056,501 - 147,066,490 (+)NCBIMGSCv36mm8
Celera2148,637,978 - 148,647,942 (+)NCBICelera
Cytogenetic Map2G2NCBI
cM Map272.63NCBI
Pax1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr83155,244,961 - 155,254,836 (+)NCBIGRCr8
mRatBN7.23134,792,330 - 134,801,637 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl3134,789,182 - 134,801,636 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx3138,710,682 - 138,720,045 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.03147,294,766 - 147,304,129 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.03144,997,920 - 145,007,281 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.03141,577,124 - 141,589,849 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl3141,577,504 - 141,589,849 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.03147,995,989 - 148,008,334 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.43136,006,504 - 136,018,849 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera3133,651,867 - 133,663,861 (+)NCBICelera
Cytogenetic Map3q41NCBI
Pax1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495541529,413,253 - 29,420,682 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495541529,413,253 - 29,420,682 (+)NCBIChiLan1.0ChiLan1.0
PAX1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v22122,594,415 - 22,607,324 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan12022,591,251 - 22,604,160 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v02021,663,155 - 21,676,880 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.12021,623,771 - 21,633,468 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl2021,623,771 - 21,632,608 (+)Ensemblpanpan1.1panPan2
PAX1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1241,742,570 - 1,752,593 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl241,743,940 - 1,753,185 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha241,769,451 - 1,778,164 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0242,148,503 - 2,157,210 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl242,147,192 - 2,157,210 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1241,746,038 - 1,754,735 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0241,848,749 - 1,857,442 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0242,124,459 - 2,134,423 (-)NCBIUU_Cfam_GSD_1.0
Pax1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024408640150,344,618 - 150,353,321 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049366203,765,444 - 3,776,467 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049366203,765,481 - 3,773,779 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
PAX1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1250,706,029 - 50,722,634 (+)NCBIChlSab1.1ChlSab1.1chlSab2
Vero_WHO_p1.0NW_0236660785,504,274 - 5,519,056 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Pax1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462474122,007,778 - 22,017,325 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462474122,009,733 - 22,017,377 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in PAX1
384 total Variants

Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

hemolymphoid system respiratory system
High
Medium
Low 1 1
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSSSCT00000007784   ⟹   ENSSSCP00000007575
Type: CODING
Position:
Pig AssemblyChrPosition (strand)Source
Sscrofa11.1 Ensembl1729,422,129 - 29,431,990 (+)Ensembl
RefSeq Acc Id: XM_021078255   ⟹   XP_020933914
Type: CODING
Position:
Pig AssemblyChrPosition (strand)Source
Sscrofa11.11729,421,117 - 29,436,481 (+)NCBI
Sequence:
Protein Sequences
Protein RefSeqs XP_020933914 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSSSCP00000007575.4
Reference Protein Sequences
RefSeq Acc Id: XP_020933914   ⟸   XM_021078255
- Sequence:
RefSeq Acc Id: ENSSSCP00000007575   ⟸   ENSSSCT00000007784
Protein Domains
Paired


Additional Information

Database Acc Id Source(s)
Ensembl Genes ENSSSCG00000007112 Ensembl, UniProtKB/TrEMBL
Ensembl Transcript ENSSSCT00000007784.4 UniProtKB/TrEMBL
Gene3D-CATH 1.10.10.10 UniProtKB/TrEMBL
InterPro Homeobox-like_sf UniProtKB/TrEMBL
  PAIRED_DNA_bd_dom UniProtKB/TrEMBL
  Paired_dom UniProtKB/TrEMBL
  PAX_fam UniProtKB/TrEMBL
  WH-like_DNA-bd_sf UniProtKB/TrEMBL
NCBI Gene PAX1 ENTREZGENE
PANTHER PTHR45636 UniProtKB/TrEMBL
  PTHR45636:SF15 UniProtKB/TrEMBL
Pfam PAX UniProtKB/TrEMBL
PRINTS PAIREDBOX UniProtKB/TrEMBL
PROSITE PAIRED_1 UniProtKB/TrEMBL
  PAIRED_2 UniProtKB/TrEMBL
SMART PAX UniProtKB/TrEMBL
Superfamily-SCOP SSF46689 UniProtKB/TrEMBL
UniProt F1SAU2_PIG UniProtKB/TrEMBL
VGNC ID VGNC:96467 ENTREZGENE